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WASHINGTON - The Obama administration’s legal team is split over how much latitude the United States has to kill Islamist militants in Yemen and Somalia, a question that could define the limits of the war against Al Qaeda and its allies, according to administration and congressional officials.

The debate, according to officials familiar with the deliberations, centers on whether the United States may take aim at a handful of high-level leaders of militant groups who are personally linked to plots to attack the United States or whether it may also attack the thousands of low-level foot soldiers focused on parochial concerns: controlling the essentially ungoverned lands near the Gulf of Aden, which separates the countries.

The dispute over limits on the use of lethal force in the region - whether from drone strikes, cruise missiles, or commando raids - has divided the State Department and the Pentagon for months, although to date it remains a theoretical disagreement. Current administration policy is to focus on “high-value individuals’’ in the region, as it has tried to do about a dozen times. But the unresolved question is whether the administration can escalate attacks against rank-and-file members of Al Qaeda in the Arabian Peninsula, based in Yemen, and the Somalia-based Al Shabab.

The answer could lay the groundwork for a shift in the fight against terrorists as the original Al Qaeda, operating out of Afghanistan and Pakistan, grows weaker. That organization has been crippled by the killing of Osama bin Laden and by a fierce campaign of drone strikes in the tribal regions of Pakistan, where the legal authority to attack militants who are battling US forces in adjoining Afghanistan is not disputed inside the administration.

One senior official played down the disagreement yesterday, characterizing it as a difference in policy emphasis, not legal views. Defense Department lawyers are trying to maintain maximum theoretical flexibility, while State Department lawyers are trying to reach out to European allies who think that there is no armed conflict, for legal purposes, outside of Afghanistan, and that the United States has a right to take action elsewhere only in self-defense, the official said.

But other officials insisted that the administration lawyers disagreed on the underlying legal authority of the United States to carry out such strikes.

Robert Chesney, a law professor at the University of Texas, Austin, who specializes in the laws of war, said the dispute reflected widespread disagreement about how to apply rules written for traditional wars to a conflict against a splintered network of terrorists - and fears that it could lead to an unending and unconstrained global war.

“It’s a tangled mess because the law is unsettled,’’ Chesney said. “Do the rules vary from location to location? Does the armed conflict exist only in the current combat zone, such as Afghanistan, or does it follow wherever participants may go? Who counts as a party to the conflict? There’s a lot at stake in these debates.’’

Counterterrorism officials have portrayed Al Qaeda in Yemen - which was responsible for the attempted bombing of a Detroit-bound airliner on Dec. 25, 2009 - as an affiliate of Al Qaeda that may be more dangerous now than the remnants of the original group. Such officials have also expressed worry about Al Shabab, although that group is generally more focused on local issues and has not been accused of attacking the United States.

In Pakistan, the United States has struck at Al Qaeda in part through “signature’’ strikes - those that are aimed at killing clusters of people whose identities are not known but who are deemed likely members of a militant group based on patterns like training in terrorist camps. The dispute over targeting could affect whether that tactic may someday be used in Yemen and Somalia, too.

The Defense Department’s general counsel, Jeh C. Johnson, has argued that the United States could significantly widen its targeting, officials said. His view, they explained, is that if a group has aligned itself with Al Qaeda, the United States can take aim at any of its combatants, especially in a country that is unable or unwilling to suppress them. The State Department’s top lawyer, Harold H. Koh, has agreed that the armed conflict with Al Qaeda is not limited to the battlefield theater of Afghanistan and adjoining parts of Pakistan. But, officials say, he has also contended that international law imposes additional constraints on the use of force elsewhere. To kill people elsewhere, he has said, the United States must be able to justify the act as necessary for its self-defense - meaning it should focus only on individuals plotting to attack the United States.

The fate of detainees at Guantanamo Bay, Cuba, hangs heavily over the targeting debate, officials said. In several habeas corpus lawsuits, judges have approved the detention of Al Qaeda suspects who were captured far from the Afghan battlefield, as well as detainees who were deemed members of a force that was merely “associated’’ with Al Qaeda. One part of the dispute is the extent to which rulings about detention are relevant to the targeting law.

Congress, too, may influence the outcome of the debate. It is considering, as part of a pending defense bill, a new authorization to use military force against Al Qaeda and its associates. A version of the provision proposed by the House Armed Forces Committee would establish an expansive standard for the categories of groups that the United States may single out for military action, potentially making it easier for the United States to kill large numbers of low-level militants in places like Somalia.